New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1912410	54 (0.690)	4 (0.050)	4/268	8.6	7.2%	coding (532/609 nt)	USA300HOU_RS15290	hypothetical protein
	?	USA300TCH1516_ALE	= 2319335	NA (NA)					coding (253/345 nt)	USA300HOU_RS15290	hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGTTGAGCGATTT  >  USA300TCH1516_ALE/1912270‑1912545                                                                                                                                             |                                                                                                                                        aTGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTg                                                                                                                                         >  1:344253/1‑141 (MQ=35) aTGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTg                                                                                                                                         >  1:291192/1‑141 (MQ=35)   gTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTa                                                                                                                                       >  1:651637/1‑141 (MQ=35)    tAGAGCCTGTTTTTGGATATGTGGTGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTAc                                                                                                                                      >  2:655403/1‑141 (MQ=255)      gagCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACAt                                                                                                                                    >  2:629124/1‑141 (MQ=35)       ggCCTGTTTTTGGATTGACGAAGGCTATTTTGGGTTCAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACAtt                                                                                                                                   <  2:429843/140‑1 (MQ=255)       cgCCTTTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACCCGACCGTCCGTTCGAGGAATAAATAAAGTTACACGATAGCTAGTTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCGCAACGAGCTGTACAtt                                                                                                                                   <  1:457629/140‑1 (MQ=11)            gTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATaaa                                                                                                                              <  2:898264/141‑1 (MQ=35)                         tGAAGGCTAGGGTGGGTTGAACTCGAACGTGAGCTAGAGGAATAAAGAAAGGGAAACGAGAGCTAGGTTGTGTATTACTGGCACTTAAAATAAGGAGGGTAGTAGCGCAACGAGCTGTACATTATAAACTACATATCaaca                                                                                                                 >  2:278810/1‑139 (MQ=2)                           aaGGGTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCaaaaaa                                                                                                               <  2:439584/141‑1 (MQ=25)                           aaGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCaaaaaa                                                                                                               <  2:170658/141‑1 (MQ=34)                           aaGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCaaaaaa                                                                                                               <  1:537016/141‑1 (MQ=35)                                   tttGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGAttt                                                                                                       >  1:750700/1‑141 (MQ=35)                                    ttGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATTGAACCGCAACGAGCTGTACATTGTAAAATACATATCAAAAAAGCTGATTTc                                                                                                      >  1:434059/1‑141 (MQ=11)                                    ttGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTgtgttc                                                                                                      >  2:642753/1‑136 (MQ=25)                                      gggTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTa                                                                                                    <  1:233923/141‑1 (MQ=35)                                      gggTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTa                                                                                                    <  2:508609/141‑1 (MQ=34)                                      gggTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTa                                                                                                    <  1:520968/141‑1 (MQ=35)                                      gggTTTAACTCAAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTa                                                                                                    <  1:924015/141‑1 (MQ=21)                                      ggatttAACTCAAACGTCAGTTCGAGTAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTa                                                                                                    <  2:262840/138‑1 (MQ=255)                                           tAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCaaa                                                                                               >  1:303357/1‑141 (MQ=34)                                           tAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCaaa                                                                                               >  1:517143/1‑141 (MQ=34)                                           tAAATCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCGAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATAAATAAAAAAAAAGCTGATTTCTATCaaa                                                                                               <  2:745275/141‑1 (MQ=11)                                            aaCTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAaat                                                                                              <  1:810375/141‑1 (MQ=33)                                            aaCTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAaat                                                                                              <  2:59438/141‑1 (MQ=32)                                              cTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAaataa                                                                                            >  2:731630/1‑141 (MQ=32)                                              cTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAaataa                                                                                            >  2:698758/1‑141 (MQ=32)                                                                                  gagaGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAAc                                                        >  2:522696/1‑141 (MQ=11)                                                                                       cTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGCACGTAAt                                                   >  2:840271/1‑141 (MQ=14)                                                                                       cTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAAt                                                   >  1:705657/1‑141 (MQ=32)                                                                                        tAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAAACAGCTTTTTTGCATTACCTAAGAACTTACTg                                                  >  2:270396/1‑141 (MQ=255)                                                                                             tttGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCa                                             >  2:367467/1‑141 (MQ=32)                                                                                                   ttAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAACTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCt                                       >  2:454513/1‑141 (MQ=17)                                                                                                     aaTGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATAAACTAATTAATAGAAATCAGCTTTTTTACACTGCCTAAGAACTTAATGTCCCAAGCCCTGa                                     <  1:629124/141‑1 (MQ=12)                                                                                                         gCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGATCTTAATGTCCCAAGCCCTGACAAt                                 <  1:590003/141‑1 (MQ=21)                                                                                                         gCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAAt                                 >  1:789969/1‑141 (MQ=34)                                                                                                           aCTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTGAATGTCCCAAGCCCTGACAATTc                               >  2:188551/1‑141 (MQ=25)                                                                                                            cTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGCACTTAATGTCCCAAGCCCTGACAATTCa                              >  1:71780/1‑141 (MQ=37)                                                                                                             ttAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCAt                             >  1:488833/1‑141 (MQ=38)                                                                                                             ttAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCAt                             >  1:140622/1‑141 (MQ=38)                                                                                                              tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATc                            >  1:604725/1‑141 (MQ=38)                                                                                                              tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATc                            >  1:568240/1‑141 (MQ=38)                                                                                                              tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATc                            >  1:243593/1‑141 (MQ=38)                                                                                                                atatAAGGAAAATAGCGGCTCAACGAGCTGTACATTATGAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTa                          >  1:513534/1‑141 (MQ=255)                                                                                                                      ggAAAATAGCAGCACAACGACCTTTACATTATAAAATACATATCAAAAAAGCTGCTTTCTATCAAATAATTAATAGAAATCAGCTTCTTTACATTGTCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCttt                    <  2:604375/141‑1 (MQ=14)                                                                                                                             agcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAGTTAATAGAAATCAGCTTTTTTACATTGCCTAGGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAg             >  2:476908/1‑141 (MQ=255)                                                                                                                             agcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAg             >  1:802085/1‑141 (MQ=255)                                                                                                                             agcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAg             >  1:754935/1‑141 (MQ=255)                                                                                                                             agcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAg             >  1:116365/1‑141 (MQ=255)                                                                                                                              gcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGt            >  1:110609/1‑141 (MQ=255)                                                                                                                              gcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACATTTTCAGCAGt            >  1:306325/1‑141 (MQ=255)                                                                                                                               cagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGtt           >  2:28887/1‑141 (MQ=255)                                                                                                                               cagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGtt           >  1:798063/1‑141 (MQ=255)                                                                                                                               cagcTCAACCAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGtt           <  2:640366/141‑1 (MQ=255)                                                                                                                                       cGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGTTGAGCGAtt   >  1:205286/1‑141 (MQ=255)                                                                                                                                        gAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGTTGAGCGAttt  >  1:893552/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                        ATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTAACTCGAACGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTTAATGTCCCAAGCCCTGACAATTCATCTAACCTTTTCATCAGTTGAGCGATTT  >  USA300TCH1516_ALE/1912270‑1912545

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.